Researchers are poised to win the race against rust diseases

A joint US and Australian research team has generated the first haplotype-resolved genome sequences for the rust fungi causing oat crown rust and wheat stripe rust diseases, two of the most destructive pathogens in oat and wheat, respectively.

After using the latest genome sequencing technologies to understand how rust fungi adapt to overcome resistance in crop varieties, scientists from the University of Minnesota, the USDA-ARS Cereal Disease Laboratory, the Australian National University, Commonwealth Scientific and Industrial Research Organisation (CSIRO) and the University of Sydney are releasing results with two publications in mBio, a journal by the American Society of Microbiology.

The work was announced (here) by the University of Minnesota.

“Like humans, rust fungi contain two copies of each chromosome, which makes their genetics much more complicated than other types of fungi,” said Assistant Professor Melania Figueroa from the University of Minnesota. Figueroa co-led the sequencing effort for the oat crown rust fungus P. coronata f. sp. avenae along with Shahryar Kianian, research leader at the USDA-ARS Cereal Disease Laboratory and adjunct professor at the University of Minnesota.

“A key advance of this work is that for the first time, separate genome assemblies were generated reflecting both of the two chromosome copies in the rust.”

In parallel, Postdoctoral Fellow Benjamin Schwessinger and Professor John Rathjen at the Australian National University applied similar approaches to develop an improved genome assembly of the stripe rust fungus, P. striiformis f. sp. tritici. By working together the two teams were able to combine their techniques and knowledge to achieve these breakthroughs much more rapidly than by working alone.

These studies represent a breakthrough in plant pathology as they now show how genetic diversity between the two chromosome copies can influence the emergence of new virulent pathogen strains.

Both studies uncovered a surprisingly high level of diversity between the two copies, suggesting that such variation likely serves as the basis to rapidly evolve new rust strains.

“Reports from growers facing yield losses due to oat crown rust occur during most cropping seasons and the genome assemblies of this pathogen will help us understand the evolution of this pathogen and means to develop more resistant crops,” said Kianian, who coordinates annual rust surveys in the US in order to monitor the pathogen population in oat growing areas.

The oat crown rust genomics study compared two strains from North Carolina and South Dakota with different virulent profiles which were obtained in 2012 as part of the routine USDA-ARS Rust Surveys.

The first author of this publication, Marisa Miller, is the awardee of a prestigious USDA-NIFA Postdoctoral Fellow and recently embarked on a study comparing the genomic composition of oat crown rust strains collected in 1990 and 2015.

“In the last 25 years the population of oat crown rust has gained additional virulences, and we would like to understand how this has occurred. Miller’s work is essential to answering this question,” commented Figueroa.

“Oat crown rust is one of the most rapidly evolving rust pathogens,” explained University of Minnesota Adjunct Professor Peter Dodds of CSIRO Agriculture and Food. “So this work will really help understand how new rust diseases like the highly destructive Ug99 race of wheat stem rust can overcome resistance in crops.”

The publications describing the work in the oat crown rust and wheat stripe rust pathogens, both released in the current issue of mBio, will serve as a framework for future studies of virulence evolution in these pathogens as well as for applying similar approaches to the rust fungi causing many other major crop diseases.


Aust researchers’ wheat genes discovery has potential to boost food security

The discovery of genes that determine the yield of flour from wheat could increase milling yield, boosting food security and producing a healthier flour.

University of Queensland researchers believe the discovery could increase the amount of flour produced from wheat by as much as 10 per cent. .

Wheat — the leading temperate climate crop — provides 20 per cent of the total calories and proteins consumed worldwide. Wheat grain is milled, or crushed, to make flour for bread and other food products.

UQ Queensland Alliance for Agriculture and Food Innovation Director Professor Robert Henry said his research team had pinpointed the genes that control a cell protein which acts like a glue, holding the wheat grain’s endosperm, wheat germ and bran layers together.

“Wheats that produce less of this glue-like protein come apart more easily in the milling process,” he said.

“This increases the efficiency of processing and improves the nutritional profile of the flour as more of the outer parts of the endosperm — rich in vitamins and minerals — are incorporated into the flour.

“This applies not only to white flour but also to wholemeal flour.

“Potentially we can take high-yielding field wheats that have not traditionally been considered suitable for milling, and turn them into milling wheats.

“This will improve on-farm production and reduce post-harvest wastage and the amount of resources used to grow the wheat.

“And, by getting a few per cent more flour from the 700 million tonnes of wheat produced globally each year, we will be producing significantly more food from the same amount of wheat,” he said.

Australian wheat traditionally attracts a high price in the market because it has a reputation of giving high flour yields.

“We haven’t been able to genetically select for this trait at early stages of breeding before,” Professor Henry said.

“The effect of this cell adhesion protein explains the difference between wheats that give us 70 per cent flour when we mill it, to 80 per cent, which is quite a big difference.”

Professor Henry said this knowledge could be employed immediately in wheat breeding programs.

“It means that we can produce premium wheats more efficiently and push the yields of quality premium wheats up.”

The team is now looking at DNA testing to breed wheats based on this new molecular discovery. Their findings are published in Scientific Reports.

Cracking manuka’s genetic code may mitigate the effects of myrtle rust

A nationwide science project that sequenced the manuka genome and is now exploring its genetic diversity may be instrumental in protecting the indigenous plant from the fungal disease myrtle rust.

Using state-of-the-art genome sequencing technologies, Plant & Food Research scientists mapped manuka’s genetic blueprint in 2015 and shared the information with tangata whenua and the New Zealand research community.

The research focus has since moved to using bioinformatic techniques to acquire a detailed understanding of the unique attributes of manuka’s genetic stocks – the data have been gleaned from around 1000 samples of manuka leaf collected nationwide in a collaboration with Landcare Research, the University of Waikato and key Maori partners.

The information generated is providing important scientific insights concerning the distribution and genetic diversity within and between manuka populations in New Zealand.

“A key objective of the project has always been to understand how genetic material is exchanged between manuka populations by pollen and seed dispersal to help whānau and hapū, and the honey industry, to develop unique stories around provenance, and help ensure genetic variation for conservation purposes,” says Plant & Food Research Science Group Leader Dr David Chagné.

“With the arrival of myrtle rust on the New Zealand mainland, we soon realised the need for an additional and more specific conservation application for the project.

“While it’s not clear just what effect myrtle rust will have on mānuka under New Zealand conditions, we should expect differences in susceptibility and resistance across the mānuka populations.

“By using the latest technologies for DNA sequencing and new methodologies for bioinformatic data analysis we can determine which parts of the genome are associated with tolerance.

“This will help us to better predict the potential damage from myrtle rust and determine how fast the various mānuka populations will respond to the disease.

“The data will assist with guiding research priorities for maintaining and protecting diversity in mānuka,” says Dr Chagné.

Research results from the project are expected to be released between June and August this year.

The Maori organisations assisting with stakeholder engagement and commercial support in the project are Ngati Porou Miere, Tuhoe Tuawhenua Trust, Atihau-Whanganui, Taitokerau Miere and Tai Tokerau Honey. The project is funded by the Ministry of Business, Innovation and Employment.

Interesting possibilities are opened by AgResearch study into “mutant” sheep

One word in the headline on an AgResearch press statement has the potential to trigger disquiet among some members of the public and perhaps whip up a lather of dismay among animal rights activists.

Let’s hope not

The headline says: “Study of mutant sheep provides exciting new opportunities”.

The press statement (here) explains that research into “mutant” sheep has AgResearch scientists eyeing up a greater understanding of what makes human hair curly or straight, and the potential for innovative new wool products.

It says the sheep, commonly known as Felting Lustre mutants, are rare and share the naturally occurring trait of straight wool, instead of the usual crimped wool.

“With these mutant sheep, we can for example look at twin lambs where one has straight wool and another crimped wool – or one animal that transforms from straight to crimped wool over time – and study the key differences,” says scientist Jeff Plowman.

“This can then be applied to our understanding of the differences in human hair. It’s an opportunity we would never have been able to get with human subjects.”

The work began in 2011, when a lamb with an unusual coat was brought to the attention of AgResearch staff involved in wool research. Its appearance was so unusual that the lamb was initially thought to be a cross between a sheep and a goat.

Part of this was because the lamb’s straight lustrous coat was reminiscent of an Angora goat.

Genetic testing showed it was 100 per cent sheep and its coat was the result of natural mutation.

“As a result, we started trying to locate more of these rare sheep, so we could study what makes them different and how proteins in the wool affect the fibres,” Dr Plowman says.

“Thanks to the assistance of farmers who came forward with these sheep, we were able to do that. We have found they show a radical change in wool structure and properties that can be tied into specific protein changes.”

“In some cases, the mutant sheep undergo a transformation where the straight wool suddenly switches to become crimpy as they mature.”

The curvature and diameter of the wool fibre are important properties in controlling performance in textiles and other products.

For example, softness, strength and felting are all affected, but the ability to control these
properties is limited because diameter and curvature are normally highly linked in sheep – low diameter means high curvature and vice versa.

“These mutant sheep are exciting because they break the mould and give us a shot at what controls each property independently, something impossible with normal sheep,” Dr Plowman says.

“People keep asking us if we are trying to breed the mutants themselves, but the situation is more complex than that. The mutant sheep, as lambs, have the same problem that Angora goat kids have – which is that they are a bit delicate, and probably not suitable for most New Zealand farms.”

“We want to use what we learn to add value to New Zealand’s mainstream sheep flocks.”

The protein differences between the mutant sheep and semi-lustrous breeds suggest that it may be possible to breed wool with controlled levels of lustre, or crimp, independent of diameter and hence produce new wool products which allow for different market opportunities.

DNA methylation is found to affect the superiority of hybrid plants

Japanese and Australian researchers have discovered that a gene involved in maintaining DNA methylation is closely connected to hybrid vigour in Arabidopsis thaliana. This has potential applications for other cruciferous vegetables such as Chinese cabbage, and could lead to more efficient breeding of high-yield vegetables.

Hybrid vigour refers to a crossbreed plant or animal showing superior traits compared to its parents.

The research group included scientists from the Graduate School of Agricultural Science, Kobe University, and Dr. Elizabeth S. Dennis and Dr. W. James Peacock from CSIRO Agriculture in Australia.

Hybrid plants have qualities useful in farming, such as increase of biomass and being stress resilient.

This AgScience blog post on the new research findings is based on a ScienceDaily report (here),  which says first-generation hybrid plants (F1 plants) bred to exhibit these hybrid vigour attributes are widely cultivated. Maize, rice and rapeseed are all F1 hybrid cultivars.

This phenomenon was discovered over 100 years ago, and is recorded in Darwin’s famous “On the Origin of Species”.

Starting from developing F1 hybrid cultivars of maize at the beginning of the 1900s, a string of hybrid agricultural crops were applied, yields increased dramatically, and the results were comparable to the “green revolution.”

But the molecular mechanisms behind this phenomenon remain unclear.

It is well known that plant traits are determined by DNA, specifically by the combination of four bases (a base sequence) of A (adenine), T (thymine), C (cytosine) and G (guamine).

In recent years, scientists have discovered that even if the DNA base sequence is the same, different traits can be observed — as you can see from looking at identical twins.

This altered expression that does not correlate with changes in the base sequence is known as epigenetic regulation (as opposed to genetic regulation). DNA methylation has been held up as one example of epigenetic regulation.

Adding or subtracting methyl to cytosine in eukaryotic organisms modifies gene expression, while the base sequence remains unchanged.

DNA also combines with histone to form a chromatin structure. DNA methylation and the change in chromatin structures caused by histone modification are both linked to modification of gene expression. Recently there have been multiple reports that hybrid vigor is influenced by epigenetic regulation as well as genetics.

Hybrid vigour can be seen in the model plant Arabidopsis thaliana (which belongs to the same Cruciferae family as Chinese cabbages). In a first generation hybrid crossed between C24 and Columbia-0 (Col), the plant has an increased biomass. However, it is still not fully understood why this F1 hybrid plant shows superior characteristics compared to its parents.

In the latest research, the team used Arabidopsis thaliana with mutations in a gene related to DNA methylation. By confirming the instances of hybrid vigor, they investigated which genes and epigenetic modifications regulating the genes were linked to hybrid vigor.

Various genes work together in regulating DNA methylation. Among them, when MET1 (Methyltransferase 1, involved in maintaining CG methylation) and Pol IV (related to RdDM, RNA directed DNA methylation, which causes de novo methylation) lost their genetic functions, abnormalities were observed in DNA methylation, but there was no observable effect on hybrid vigor. However, in an F1 hybrid created using a plant with a non-functional DDM1 chromatin remodeling factor (involved in maintaining DNA methylation by modifying chromatin structure), abnormalities were seen in DNA methylation, and the level of hybrid vigor was significantly lower.

This demonstrated that DDM1 and hybrid vigour are closely linked, and the epigenetic modification regulated by DDM1 (DNA methylation) is important in hybrid vigor. There have been few concrete reports of the genes involved in hybrid vigou, but based on this research, one of the key genes for hybrid vigour has been clarified.

Currently the research team is preparing to comprehensively analyse the changes in DNA methylation caused by loss of DDM1 function and the accompanying changes in DNA expression level. Based on these findings, they plan to conclusively identify the genes that regulate hybrid vigour.

Arabidopsis thaliana is a cruciferous plant, which means that the knowledge gained through this research can be applied to other plants in this family such as Chinese cabbage, cabbage, broccoli, and rapeseed. This could potentially be used to breed high-yield crop cultivars. The team is also investigating hybrid vigour using Chinese cabbage.


Sheep Central Progeny Test extends to commercial properties

Beef + Lamb New Zealand (B+LNZ) Genetics is increasing the breadth of testing for genetic potential in New Zealand sheep by adjusting the focus of its Central Progeny Test (CPT) to increase relevance for commercial flocks.

The goal is to help breeders and commercial farmers more easily identify top genetics that will

  • Perform best in their environment, particularly hill country;
  • Increase the number and diversity of locations in which testing occurs;
  • Increase the number of rams tested; and increase the connectedness of ram breeding flocks across the country.

The main objectives of these developments are to:

  •  Assess the genetic potential of progeny in country that more accurately reflects the environment in which sheep are increasingly farmed (characterised as North Island hill country, dry hill country and South Island hill country).
  •  Shift the focus to “Next Generation” sires by testing progeny of up-and-coming rams selected on potential genetic merit, rather than relying on older sires that already have progeny.
  •  Increase the numbers of rams tested to increase flock connectedness (linkages) and allow breeders and commercial farmers to more accurately compare rams to increase genetic gain.
  • Achieve greater transparency through direct commercial farmer engagement at on-farm field days.

The first Next Generation flock will be established on a Horizon Farming Ltd property in the Hawke’s Bay. It will have a terminal sire focus and evaluate leading young rams that are not yet progeny-proven.

B+LNZ Genetics General Manager Graham Alder says the developments in the Sheep CPT are, in part, inspired by the positive experience of involving commercial farms in the Beef CPT programme. It also reflects widespread feedback from leading sheep stud breeders and commercial farmers.

Alder says:

“The message and underlying logic is pretty clear. Progeny testing can be improved and the speed of genetic gain increased by upping the numbers of rams tested on real-life commercial farming sites. This is an important part of our strategy for lifting the rate of genetic gains across the industry.”

All sites will follow best practise in animal management and will make use of advances in on-farm measuring and monitoring technology to aid data collection and data accuracy.

Alder says:

“It’s fair to say that, technologically speaking, even five years ago extending CPT to a commercial environment would have been a major challenge. What’s more, further developments in measuring and recording technology – by companies like Tru-Test and Gallagher, along with DNA parentage from Zoetis – allow us to run the programme in commercial flocks.”

Over the next three years, CPT work at the lowland sites of Poukawa (Hawke’s Bay) and Ashley Dene (Canterbury) will be phased out, with testing increasingly moving to commercial farms and involving significantly larger numbers of rams. The three other existing test sites – Woodlands in Southland and the hill sites of Onslow View in Central Otago and Taratahi Agricultural Training Centre in the Wairarapa – are set to continue as previously.


Redefining genetic modification – Science Media Centre gathers expert reactions

The Environmental Protection Authority is planning to tweak regulations to clear up confusion over what is and is not a genetically modified organism (GMO).

Under current law, widely-used crops can be considered “genetically modified” because of the way they were created, despite having been grown in New Zealand fields for decades.

The proposed amendments clarify that organisms and plants bred using conventional chemical and radiation treatments are not considered genetically modified under the law. These older breeding technologies were in use in New Zealand before restrictions on GMOs were put in place in 1998 and are common overseas.

The issue was raised by the High Court during a controversial court case last year which centred on the definition of GMOs.

The Science Media Centre collected the following expert commentary.

Prof Barry Scott, Professor of Molecular Genetics, Massey University, comments:

“I welcome the decision by the Environmental Protection Agency (EPA) to review the regulations under the HSNO Act to clarify what is not a genetically modified organism. Decisions like this should not be made in the High Court, as was the case in May of last year around a determination sought by Scion from EPA where the decision made by EPA was subsequently overturned in the High Court.

“It is now 40 years since the development of recombinant DNA technologies and 20 years since passage of the HSNO Act. Our knowledge of the science and the technologies themselves have advanced significantly in this period yet research in New Zealand is caught in what essentially is a time warp. Clarity around what is not a GMO is very much a first and essential step to address to avoid legal redress as occurred last year.

“However, a more general overhaul of the regulations is urgently needed for New Zealand to take advantage of the very significant advances that have taken place. The highly risk averse nature of the current New Zealand regulations are way out of step with the current scientific knowledge available on GM technologies and the regulations and practices in most international jurisdictions. This disjoint has led to a compliance regime that is excessive to what is needed to manage the low risk nature of most of the current GM techniques and technologies.”

Prof Jack Heinemann, Lecturer in Genetics, University of Canterbury, comments:

“The EPA proposal is needed to improve the clarity of the HSNO Act. The EPA proposal also helps to remove uncertainty about forms of chemical mutagenesis in use prior to 1998, and whether or not the products of these kinds of modifications should be regulated by HSNO.

“I see no additional impact of great relevance to either research or industry from the proposed revisions, because the changes are aligned with how most of us had interpreted the rules anyway.

Dr Elspeth MacRae, General Manager Manufacturing and Bioproducts, Scion comments:

“It is a fallacy that NZ is GMO-free and always has been, when we have food ingredients on our shelves produced using GMO and we wear and use cotton which is mostly GMO fibre, and we eat cheese and other foods that have been made using GMO microbes. …

“The legislation is now almost two decades old and well out of step with the rapid advancement in science and the large amount of scientific evidence regarding the risks and benefits of genetic technologies. …

“Scientifically and commercially the benefits of genetic technologies have outweighed risks (recorded in multiple analyses after over 20 years of commercial and scientific activity). New Zealand needs to be able to responsibly choose genetic options for the future based on the scientific evidence.

“Since the legislation was introduced, we have become very risk averse; costs for applications for permission to evaluate technologies has risen sharply and, as evidenced by the reduction in field trials under containment, this is blocking innovation and opportunities that should be explored. …

“In its current interpretation the law says many plants currently growing in New Zealand are now defined as GMOs. This means that in essence many people are growing such plants illegally because they have not gone through the proper EPA process.

“However, much more change is needed to the legislation to make it workable and less costly for research and business, and to promote true evaluation of the opportunities that allows benefits and risks to be assessed.

“New Zealand is a biological country and is likely to miss opportunities to capitalise on the benefits on GMO plants, including impacts that are positive for climate change and greenhouse gas emissions and our future liabilities under Kyoto and later agreements.”

The Science Media Centre has abridged these comments – the full comments are available on its website.
Assoc Prof Peter Dearden, Director of Genetics Otago, comments:

“The EPA is seeking submissions on a change to the legislation which is driven by a high court decision last year that indicated problems with the current legislation. What was pointed out by the high court is that commonly and widely used techniques, not thought of as genetic modification, are not exempt from the legislation, even though that was the intention.

“Normal selective breeding requires breeders to identify variant plants or animals, and select those with desirable characteristics. If there is not enough variation, or not the variation that is wanted, breeders can use radiation or chemical mutagens to make new variants. These chemicals or radiation cause small changes in DNA in random places, producing variants that can then be selected. These techniques are commonly used and underpin, for example, the green revolution, which had a huge positive impact in food production.

“The current legislation suggests that these techniques should be classed as genetic modification, and the organisms involved treated as genetically modified. This would have a huge effect on plant breeding and food production in particular in New Zealand, as most new varieties of plants are produced in this way.

“The changes suggested by the EPA will tidy up this problem, and will not affect the way we currently deal with genetic modification in industry or research.”

Declarations of interest:

Elspeth McCrae: Scion is involved in research using genetic modification and its EPA application was the subject of the High Court case mentioned above.

No other declarations received.